LOCUS       NM_020246               3315 bp    mRNA    linear   PRI 06-JUN-2024
DEFINITION  Homo sapiens solute carrier family 12 member 9 (SLC12A9),
            transcript variant 1, mRNA.
ACCESSION   NM_020246
VERSION     NM_020246.4
KEYWORDS    RefSeq; MANE Select.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 3315)
  AUTHORS   Accogli,A., Park,Y.N., Lenk,G.M., Severino,M., Scala,M.,
            Denecke,J., Hempel,M., Lessel,D., Kortum,F., Salpietro,V., de
            Marco,P., Guerrisi,S., Torella,A., Nigro,V., Srour,M., Turro,E.,
            Labarque,V., Freson,K., Piatelli,G., Capra,V., Kitzman,J.O. and
            Meisler,M.H.
  TITLE     Biallelic loss-of-function variants of SLC12A9 cause lysosome
            dysfunction and a syndromic neurodevelopmental disorder
  JOURNAL   Genet Med 26 (5), 101097 (2024)
   PUBMED   38334070
  REMARK    GeneRIF: Biallelic loss-of-function variants of SLC12A9 cause
            lysosome dysfunction and a syndromic neurodevelopmental disorder.
REFERENCE   2  (bases 1 to 3315)
  AUTHORS   Du,W., Xia,G., Chen,L., Geng,L., Xu,R., Han,Q., Ying,X. and Yu,H.
  TITLE     Clinical value of SLC12A9 for diagnosis and prognosis in colorectal
            cancer
  JOURNAL   Aging (Albany NY) 15 (24), 15419-15433 (2023)
   PUBMED   38157260
  REMARK    GeneRIF: Clinical value of SLC12A9 for diagnosis and prognosis in
            colorectal cancer.
REFERENCE   3  (bases 1 to 3315)
  AUTHORS   Yan,C., Hu,X., Liu,X., Zhao,J., Le,Z., Feng,J., Zhou,M., Ma,X.,
            Zheng,Q. and Sun,J.
  TITLE     Upregulation of SLC12A3 and SLC12A9 Mediated by the HCP5/miR-140-5p
            Axis Confers Aggressiveness and Unfavorable Prognosis in Uveal
            Melanoma
  JOURNAL   Lab Invest 103 (3), 100022 (2023)
   PUBMED   36925204
  REMARK    GeneRIF: Upregulation of SLC12A3 and SLC12A9 Mediated by the
            HCP5/miR-140-5p Axis Confers Aggressiveness and Unfavorable
            Prognosis in Uveal Melanoma.
REFERENCE   4  (bases 1 to 3315)
  AUTHORS   Gagnon,K.B. and Delpire,E.
  TITLE     Physiology of SLC12 transporters: lessons from inherited human
            genetic mutations and genetically engineered mouse knockouts
  JOURNAL   Am J Physiol Cell Physiol 304 (8), C693-C714 (2013)
   PUBMED   23325410
  REMARK    GeneRIF: Review summarizes three human disorders that have been
            linked to the mutation/dysfunction of Na-Cl, Na-K-2Cl, and K-Cl
            cotransporters (Bartter's, Gitleman's, and Andermann's syndromes).
            Review article
REFERENCE   5  (bases 1 to 3315)
  AUTHORS   Huang,J., Sabater-Lleal,M., Asselbergs,F.W., Tregouet,D.,
            Shin,S.Y., Ding,J., Baumert,J., Oudot-Mellakh,T., Folkersen,L.,
            Johnson,A.D., Smith,N.L., Williams,S.M., Ikram,M.A., Kleber,M.E.,
            Becker,D.M., Truong,V., Mychaleckyj,J.C., Tang,W., Yang,Q.,
            Sennblad,B., Moore,J.H., Williams,F.M., Dehghan,A., Silbernagel,G.,
            Schrijvers,E.M., Smith,S., Karakas,M., Tofler,G.H., Silveira,A.,
            Navis,G.J., Lohman,K., Chen,M.H., Peters,A., Goel,A.,
            Hopewell,J.C., Chambers,J.C., Saleheen,D., Lundmark,P., Psaty,B.M.,
            Strawbridge,R.J., Boehm,B.O., Carter,A.M., Meisinger,C.,
            Peden,J.F., Bis,J.C., McKnight,B., Ohrvik,J., Taylor,K.,
            Franzosi,M.G., Seedorf,U., Collins,R., Franco-Cereceda,A.,
            Syvanen,A.C., Goodall,A.H., Yanek,L.R., Cushman,M.,
            Muller-Nurasyid,M., Folsom,A.R., Basu,S., Matijevic,N., van
            Gilst,W.H., Kooner,J.S., Hofman,A., Danesh,J., Clarke,R.,
            Meigs,J.B., Kathiresan,S., Reilly,M.P., Klopp,N., Harris,T.B.,
            Winkelmann,B.R., Grant,P.J., Hillege,H.L., Watkins,H.,
            Spector,T.D., Becker,L.C., Tracy,R.P., Marz,W., Uitterlinden,A.G.,
            Eriksson,P., Cambien,F., Morange,P.E., Koenig,W., Soranzo,N., van
            der Harst,P., Liu,Y., O'Donnell,C.J. and Hamsten,A.
  CONSRTM   DIAGRAM Consortium; CARDIoGRAM Consortium; C4D Consortium;
            CARDIOGENICS Consortium
  TITLE     Genome-wide association study for circulating levels of PAI-1
            provides novel insights into its regulation
  JOURNAL   Blood 120 (24), 4873-4881 (2012)
   PUBMED   22990020
REFERENCE   6  (bases 1 to 3315)
  AUTHORS   Eijgelsheim,M., Newton-Cheh,C., Sotoodehnia,N., de Bakker,P.I.,
            Muller,M., Morrison,A.C., Smith,A.V., Isaacs,A., Sanna,S., Dorr,M.,
            Navarro,P., Fuchsberger,C., Nolte,I.M., de Geus,E.J., Estrada,K.,
            Hwang,S.J., Bis,J.C., Ruckert,I.M., Alonso,A., Launer,L.J.,
            Hottenga,J.J., Rivadeneira,F., Noseworthy,P.A., Rice,K.M., Perz,S.,
            Arking,D.E., Spector,T.D., Kors,J.A., Aulchenko,Y.S., Tarasov,K.V.,
            Homuth,G., Wild,S.H., Marroni,F., Gieger,C., Licht,C.M.,
            Prineas,R.J., Hofman,A., Rotter,J.I., Hicks,A.A., Ernst,F.,
            Najjar,S.S., Wright,A.F., Peters,A., Fox,E.R., Oostra,B.A.,
            Kroemer,H.K., Couper,D., Volzke,H., Campbell,H., Meitinger,T.,
            Uda,M., Witteman,J.C., Psaty,B.M., Wichmann,H.E., Harris,T.B.,
            Kaab,S., Siscovick,D.S., Jamshidi,Y., Uitterlinden,A.G.,
            Folsom,A.R., Larson,M.G., Wilson,J.F., Penninx,B.W., Snieder,H.,
            Pramstaller,P.P., van Duijn,C.M., Lakatta,E.G., Felix,S.B.,
            Gudnason,V., Pfeufer,A., Heckbert,S.R., Stricker,B.H.,
            Boerwinkle,E. and O'Donnell,C.J.
  TITLE     Genome-wide association analysis identifies multiple loci related
            to resting heart rate
  JOURNAL   Hum Mol Genet 19 (19), 3885-3894 (2010)
   PUBMED   20639392
  REMARK    GeneRIF: Observational study, meta-analysis, and genome-wide
            association study of gene-disease association. (HuGE Navigator)
REFERENCE   7  (bases 1 to 3315)
  AUTHORS   Gonzales,P.A., Pisitkun,T., Hoffert,J.D., Tchapyjnikov,D.,
            Star,R.A., Kleta,R., Wang,N.S. and Knepper,M.A.
  TITLE     Large-scale proteomics and phosphoproteomics of urinary exosomes
  JOURNAL   J Am Soc Nephrol 20 (2), 363-379 (2009)
   PUBMED   19056867
REFERENCE   8  (bases 1 to 3315)
  AUTHORS   Wilson,M.D., Riemer,C., Martindale,D.W., Schnupf,P., Boright,A.P.,
            Cheung,T.L., Hardy,D.M., Schwartz,S., Scherer,S.W., Tsui,L.C.,
            Miller,W. and Koop,B.F.
  TITLE     Comparative analysis of the gene-dense ACHE/TFR2 region on human
            chromosome 7q22 with the orthologous region on mouse chromosome 5
  JOURNAL   Nucleic Acids Res 29 (6), 1352-1365 (2001)
   PUBMED   11239002
REFERENCE   9  (bases 1 to 3315)
  AUTHORS   de Vries,H., Ruegsegger,U., Hubner,W., Friedlein,A., Langen,H. and
            Keller,W.
  TITLE     Human pre-mRNA cleavage factor II(m) contains homologs of yeast
            proteins and bridges two other cleavage factors
  JOURNAL   EMBO J 19 (21), 5895-5904 (2000)
   PUBMED   11060040
REFERENCE   10 (bases 1 to 3315)
  AUTHORS   Caron,L., Rousseau,F., Gagnon,E. and Isenring,P.
  TITLE     Cloning and functional characterization of a cation-Cl-
            cotransporter-interacting protein
  JOURNAL   J Biol Chem 275 (41), 32027-32036 (2000)
   PUBMED   10871601
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AC011895.4.
            
            On Nov 23, 2018 this sequence version replaced NM_020246.3.
            
            Transcript Variant: This variant (1) represents the longest
            transcript and encodes the longest isoform (1).
            
            ##Evidence-Data-START##
            Transcript exon combination :: AB033284.1, AF284422.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000354161.8/ ENSP00000275730.4
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-123               AC011895.4         94846-94968
            124-346             AC011895.4         96289-96511
            347-481             AC011895.4         96753-96887
            482-613             AC011895.4         97839-97970
            614-922             AC011895.4         99001-99309
            923-1030            AC011895.4         100968-101075
            1031-1142           AC011895.4         101183-101294
            1143-1300           AC011895.4         102018-102175
            1301-1383           AC011895.4         102283-102365
            1384-1508           AC011895.4         103271-103395
            1509-1701           AC011895.4         103525-103717
            1702-1876           AC011895.4         103870-104044
            1877-2023           AC011895.4         104814-104960
            2024-3315           AC011895.4         107852-109143
FEATURES             Location/Qualifiers
     source          1..3315
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="7"
                     /map="7q22.1"
     gene            1..3315
                     /gene="SLC12A9"
                     /gene_synonym="CCC6; CIP1; hCCC6; WO3.3"
                     /note="solute carrier family 12 member 9"
                     /db_xref="GeneID:56996"
                     /db_xref="HGNC:HGNC:17435"
                     /db_xref="MIM:616861"
     exon            1..123
                     /gene="SLC12A9"
                     /gene_synonym="CCC6; CIP1; hCCC6; WO3.3"
                     /inference="alignment:Splign:2.1.0"
     exon            124..346
                     /gene="SLC12A9"
                     /gene_synonym="CCC6; CIP1; hCCC6; WO3.3"
                     /inference="alignment:Splign:2.1.0"
     CDS             166..2910
                     /gene="SLC12A9"
                     /gene_synonym="CCC6; CIP1; hCCC6; WO3.3"
                     /note="isoform 1 is encoded by transcript variant 1;
                     cation-chloride cotransporter-interacting protein 1;
                     CCC-interacting protein 1; cation-chloride cotransporter
                     6; potassium-chloride transporter 9; solute carrier family
                     12 (potassium/chloride transporters), member 9"
                     /codon_start=1
                     /product="solute carrier family 12 member 9 isoform 1"
                     /protein_id="NP_064631.2"
                     /db_xref="CCDS:CCDS5707.1"
                     /db_xref="GeneID:56996"
                     /db_xref="HGNC:HGNC:17435"
                     /db_xref="MIM:616861"
                     /translation="MASESSPLLAYRLLGEEGVALPANGAGGPGGASARKLSTFLGVV
                     VPTVLSMFSIVVFLRIGFVVGHAGLLQALAMLLVAYFILALTVLSVCAIATNGAVQGG
                     GAYFMISRTLGPEVGGSIGLMFYLANVCGCAVSLLGLVESVLDVFGADATGPSGLRVL
                     PQGYGWNLLYGSLLLGLVGGVCTLGAGLYARASFLTFLLVSGSLASVLISFVAVGPRD
                     IRLTPRPGPNGSSLPPRFGHFTGFNSSTLKDNLGAGYAEDYTTGAVMNFASVFAVLFN
                     GCTGIMAGANMSGELKDPSRAIPLGTIVAVAYTFFVYVLLFFLSSFTCDRTLLQEDYG
                     FFRAISLWPPLVLIGIYATALSASMSSLIGASRILHALARDDLFGVILAPAKVVSRGG
                     NPWAAVLYSWGLVQLVLLAGKLNTLAAVVTVFYLVAYAAVDLSCLSLEWASAPNFRPT
                     FSLFSWHTCLLGVASCLLMMFLISPGAAGGSLLLMGLLAALLTARGGPSSWGYVSQAL
                     LFHQVRKYLLRLDVRKDHVKFWRPQLLLLVGNPRGALPLLRLANQLKKGGLYVLGHVT
                     LGDLDSLPSDPVQPQYGAWLSLVDRAQVKAFVDLTLSPSVRQGAQHLLRISGLGGMKP
                     NTLVLGFYDDAPPQDHFLTDPAFSEPADSTREGSSPALSTLFPPPRAPGSPRALNPQD
                     YVATVADALKMNKNVVLARASGALPPERLSRGSGGTSQLHHVDVWPLNLLRPRGGPGY
                     VDVCGLFLLQMATILGMVPAWHSARLRIFLCLGPREAPGAAEGRLRALLSQLRIRAEV
                     QEVVWGEGAGAGEPEAEEEGDFVNSGRGDAEAEALARSANALVRAQQGRGTGGGPGGP
                     EGGDAEGPITALTFLYLPRPPADPARYPRYLALLETLTRDLGPTLLVHGVTPVTCTDL
                     "
     exon            347..481
                     /gene="SLC12A9"
                     /gene_synonym="CCC6; CIP1; hCCC6; WO3.3"
                     /inference="alignment:Splign:2.1.0"
     exon            482..613
                     /gene="SLC12A9"
                     /gene_synonym="CCC6; CIP1; hCCC6; WO3.3"
                     /inference="alignment:Splign:2.1.0"
     exon            614..922
                     /gene="SLC12A9"
                     /gene_synonym="CCC6; CIP1; hCCC6; WO3.3"
                     /inference="alignment:Splign:2.1.0"
     exon            923..1030
                     /gene="SLC12A9"
                     /gene_synonym="CCC6; CIP1; hCCC6; WO3.3"
                     /inference="alignment:Splign:2.1.0"
     exon            1031..1142
                     /gene="SLC12A9"
                     /gene_synonym="CCC6; CIP1; hCCC6; WO3.3"
                     /inference="alignment:Splign:2.1.0"
     exon            1143..1300
                     /gene="SLC12A9"
                     /gene_synonym="CCC6; CIP1; hCCC6; WO3.3"
                     /inference="alignment:Splign:2.1.0"
     exon            1301..1383
                     /gene="SLC12A9"
                     /gene_synonym="CCC6; CIP1; hCCC6; WO3.3"
                     /inference="alignment:Splign:2.1.0"
     exon            1384..1508
                     /gene="SLC12A9"
                     /gene_synonym="CCC6; CIP1; hCCC6; WO3.3"
                     /inference="alignment:Splign:2.1.0"
     exon            1509..1701
                     /gene="SLC12A9"
                     /gene_synonym="CCC6; CIP1; hCCC6; WO3.3"
                     /inference="alignment:Splign:2.1.0"
     exon            1702..1876
                     /gene="SLC12A9"
                     /gene_synonym="CCC6; CIP1; hCCC6; WO3.3"
                     /inference="alignment:Splign:2.1.0"
     exon            1877..2023
                     /gene="SLC12A9"
                     /gene_synonym="CCC6; CIP1; hCCC6; WO3.3"
                     /inference="alignment:Splign:2.1.0"
     exon            2024..3315
                     /gene="SLC12A9"
                     /gene_synonym="CCC6; CIP1; hCCC6; WO3.3"
                     /inference="alignment:Splign:2.1.0"
     regulatory      3296..3301
                     /regulatory_class="polyA_signal_sequence"
                     /gene="SLC12A9"
                     /gene_synonym="CCC6; CIP1; hCCC6; WO3.3"
                     /note="hexamer: AATAAA"
     polyA_site      3315
                     /gene="SLC12A9"
                     /gene_synonym="CCC6; CIP1; hCCC6; WO3.3"
                     /note="major polyA site"
ORIGIN      
        1 ggggacaggc tccaggcctg gcatcccggt agccgcagct gtcttttccg gcccccgtgc
       61 actctccgcc cgagcggagc cccccggctc gcggggatcg cccccgagcg ctgcgtcctg
      121 cgggtcacct aacccatttg tggcttcctc tacctgtgct cagccatggc cagcgagagc
      181 tcacctctgc tggcctaccg gctcctgggg gaggaggggg ttgccctccc tgccaatggg
      241 gccgggggtc ctggaggggc gtctgcccgg aagctgtcca ccttcctggg tgtggtggtg
      301 cccactgtcc tgtccatgtt cagcatagtt gtttttctga ggattgggtt cgtggtgggt
      361 catgctgggc tactgcaggc cctggccatg ctgctggttg cctacttcat cctggcactc
      421 accgtcctct ctgtctgtgc catcgccacc aatggagccg tgcagggggg cggagcctac
      481 ttcatgatca gccgcacact ggggcccgag gtcgggggca gcattgggct catgttctac
      541 ctggctaacg tctgtggctg tgccgtctcc ctcctggggc tggtggagtc tgtgcttgat
      601 gtcttcgggg ccgatgccac agggcccagt gggctccggg tcctgcccca gggctacggc
      661 tggaacctgc tgtatggctc cctgctgctg ggccttgtgg gtggggtctg caccctggga
      721 gccggcctct atgcccgggc ctcattcctc acattcctgc tggtctctgg ctccctggcc
      781 tctgtgctca tcagttttgt ggctgtgggg ccgagggaca tccgcttgac tcctaggcct
      841 ggccccaatg gctcctccct gccgccccgg tttggccact tcaccggctt caacagcagt
      901 accctgaagg acaacttggg cgctggctat gctgaggact acaccacggg agccgtgatg
      961 aattttgcca gcgtctttgc tgtcctcttt aacggctgta caggcatcat ggctggggcc
     1021 aacatgtcag gggagctgaa ggaccccagc cgggcgatcc ctctgggcac gatcgtcgcc
     1081 gtcgcctaca ccttcttcgt ctatgtcctg cttttctttc tctccagctt cacttgtgac
     1141 aggaccctgc tgcaggaaga ctatgggttc ttccgcgcca tcagcctgtg gcccccactg
     1201 gtgttgatcg gaatctatgc cacagcgctc tcagcgtcca tgagctcgct cattggtgcc
     1261 tcccgcatcc tccatgccct ggcccgggat gacctctttg gcgtgatctt ggcaccggcc
     1321 aaggttgtgt cccgaggggg aaacccctgg gcagctgtac tttattcttg gggcctggtg
     1381 cagctggtgc tcctggctgg gaagctgaac acactggctg ctgtggtcac tgtcttctac
     1441 ctggtggcct atgctgccgt ggacctgtcc tgcctgagcc tggagtgggc ctcggccccc
     1501 aacttccgcc ccaccttcag cctgttctcc tggcacacct gcctgctggg ggtggcctcc
     1561 tgcctgctca tgatgttcct catcagtcct ggcgcggctg gtggctccct gctcctcatg
     1621 ggtctgctgg ctgccctgct caccgcgcga ggaggcccca gtagctgggg ctatgtcagc
     1681 caggccttgc ttttccacca ggtgcgtaag tatctgcttc ggctggacgt ccggaaggat
     1741 cacgtgaagt tctggcggcc ccagctgctg ctcctggtgg ggaacccccg gggcgccctg
     1801 cctctgctgc ggttggccaa ccagcttaag aagggggggc tgtatgtgct gggccacgtc
     1861 accctgggag acctcgactc cctgccctcg gaccctgtac agccgcagta tggggcatgg
     1921 ctcagcctgg tggaccgtgc ccaggtgaag gcttttgtgg atctaaccct ctcaccctcc
     1981 gtgcgccagg gggctcagca tctgctgcga atctccggcc tcggtggcat gaagcccaac
     2041 acgttggtcc taggtttcta cgatgacgct ccaccgcagg accatttcct gacggacccg
     2101 gctttctctg agcctgcaga cagcaccagg gagggcagtt ccccagctct gagcaccctg
     2161 ttccctcctc cccgggctcc tgggagcccc cgggccctca atccccagga ctatgtggcc
     2221 acggtggccg acgccctcaa gatgaacaag aatgtggtgc tggcccgggc cagcggggcc
     2281 ttgccccctg agcggctgag ccgggggtct gggggcacct ctcagctgca ccatgtggac
     2341 gtgtggcccc tcaacctgct gcggccccgg ggtgggcccg gctatgtgga tgtctgcggc
     2401 ctcttcctgc tgcagatggc aaccatcttg ggcatggtgc ccgcttggca tagcgcccgg
     2461 ctccggatct tcctgtgcct ggggcctcgg gaggcgcctg gggcggccga ggggcggctg
     2521 cgggcactgc tgagccaact gaggatccgg gctgaggtgc aggaggtggt gtggggcgag
     2581 ggggccgggg ctggggaacc cgaggcggag gaggaagggg actttgtgaa cagtgggcgg
     2641 ggagacgcag aggcagaggc cctggcacgc agcgccaacg ccctggttcg ggcccagcag
     2701 gggcgcggca caggaggagg gccgggtggg ccggagggtg gggatgctga gggccccatc
     2761 acagccctca ccttcctgta cttgcctcgg ccgccagccg atcccgcccg atacccccgc
     2821 tacctggcgc tactggagac tctaacccga gacctgggcc ccacgctgct ggttcatggg
     2881 gtcactccag tcacctgcac tgatctgtga tgcccctgcc tccagggcta ggtagagagg
     2941 gcccaggcag gcggcctatc ctgatccttg gaggaggagg aagaggaggc cactgtggcc
     3001 cgtggccctg cccttgggac gtggagccca ggggaggttt gaaggggatc ctgggcttgg
     3061 gcatcacgcc cacctccttt ggcagaggga ccccagcaca ctaactctgg gtggctgtcc
     3121 ccaccgtgca ggggagggag tccgcagcct cccttcactg gtgccttgat gctaggggcc
     3181 aggcctcctc tgtgactctg ggctacctca gtttccccat tttggccaga ctcaccggcc
     3241 cactggggtg gtgatgtttt cgttctgttt tatttttcta actctgctga ccatgaataa
     3301 aagaccaaaa cacta
//
